Got a MB QUART WM1-CD head unit with Front and Rear RCA line outs. My amp is 800watts, 4 channels and I am trying to push 6 Exile SX65Ms. When I plug the Rear line out into the amp Rear RCA connectors, the volume is incredibly loud, even though the head unit volume is only set to “2” on the head unit. I have the gain level on the Rear channel of the amp set to the bare minimum, and it’s still way too loud. What might cause this?

Need info on the amp. There could be an input on the amp that is essentially line level input that doesn't have any volume control. You may also have something on the amp checked or adjusted wrong.
I'm guessing the issue is amp related, not head unit related.
Generally speaking, the signal being put out from the RCAs of the head unit is low and in need of an amp to boost it.

Ok, so assuming these are your only speakers and you don't have a sub, towers or anything, here's my recommendation.

Wire up 1 pair of speakers on the front terminals
Wire up 2 pairs of speakers to the rear terminals
Amp switched to 4 channel mode
Leave both switched to full
turn down the gains and slowly turn them up

If you find there is too much bass coming through, turn on the low pass filter, put it to around 60-80hz this will filter out the sub bass, but leave in the mid bass.
If you find there is too much highs coming through (unlikely) turn on the high pass filter and tune it down until you are no longer hearing it sound tinny.

Depending on how you have the speakers hooked up, you may have too little resistance on the amp and it is getting way too much signal. This setup would put your fronts to 4 ohm and the rears to 2 ohm.